diff --git a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf
index 84a029b30754..1ebada6e0d2e 100644
--- a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf
+++ b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf
@@ -257,6 +257,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS {
         BBMAP_BBSPLIT.out.primary_fastq.set { ch_filtered_reads }
 
         ch_versions = ch_versions.mix(BBMAP_BBSPLIT.out.versions.first())
+        ch_multiqc_files = ch_multiqc_files.mix(BBMAP_BBSPLIT.out.stats)
 
         if (!skip_linting) {
             FQ_LINT_AFTER_BBSPLIT(